def _test():
"""Tests"""
import ClearMap.Settings as settings
import ClearMap.IO.IO as io
import ClearMap.Visualization.Plot3d as p3d;
import ClearMap.Alignment.Resampling as res
from importlib import reload
reload(res)
r = res.resample_shape(source_shape=(100,200,300), sink_shape=(50,50,30));
print('resampled source_shape=%r, sink_shape=%r, source_resolution=%r, sink_resolution=%r' % r)
r = res.resample_shape(source_shape=(100,200,300), source_resolution=(2,2,2), sink_resolution=(10,2,1))
print('resampled source_shape=%r, sink_shape=%r, source_resolution=%r, sink_resolution=%r' % r)
source = io.join(settings.test_data_path, 'Resampling/test.tif')
sink = io.join(settings.test_data_path, "Resampling/resampled.npy")
source = io.join(settings.test_data_path, 'Tif/sequence/sequence<Z,4>.tif')
sink = io.join(settings.test_data_path, "Resampling/resampled_sequence.tif")
source_shape, sink_shape, source_res, sink_res = res.resample_shape(source_shape=io.shape(source), source_resolution=(1.,1.,1.), sink_resolution=(1.6,1.6,2))
axes_order = res._axes_order(None, source_shape, sink_shape);
print(axes_order)
resampled = res.resample(source, sink, source_resolution=(1.,1.,1.), sink_resolution = (1.6,1.6,2), orientation=None, processes=None);
p3d.plot(resampled)
p3d.plot(source)
inverse = res.resample_inverse(resampled, sink=None, resample_source=source, source_resolution=(1,1,1), sink_resolution = (10,10,2), orientation=None, processes='serial')
p3d.plot([source, inverse])
resampled = res.resample(source, sink, source_resolution=(1,1,1), sink_resolution = (10,10,2), orientation=(2,-1,3), processes=None);
p3d.plot(resampled)
inverse = res.resample_inverse(resampled, sink=None, resample_source=source, source_resolution=(1,1,1), sink_resolution = (10,10,2), orientation=(2,-1,3), processes=None)
p3d.plot([source, inverse])
resampled = res.resample(source, sink=None, source_resolution=(1.6,1.6,2), sink_shape=(10,20,30), orientation=None, processes=None)
p3d.plot(resampled)
# ponints
points = res.np.array([[0,0,0], [1,1,1], [1,2,3]], dtype=float);
resampled_points = res.resample_points(points, resample_source=source , resample_sink=sink, orientation=None)
print(resampled_points)
inverse_points = res.resample_points_inverse(resampled_points, resample_source=source , resample_sink=sink, orientation=None)
print(inverse_points)
print(res.np.allclose(points, inverse_points))
def filename(ftype, file_type_to_name = None, directory = None, expression = None, values = None, prefix = None, postfix = None, extension = None, debug = None):
"""Returns the standard file name to use for a result file.
Arguments
---------
ftype : str
The type of the file for which the file name is requested.
directory : str
The working directory of the project.
expression : str or None
The tag expression to use if ftype is 'expression'.
file_type_to_name : dict
The file types to name mappings. If None, the default is used.
values : dict or None
The values to use in case a tag expression is given.
prefix : str or None
Optional prefix to the file if not None.
postfix : str or list of str or None
Optional postfix to the file if not None.
extension : str or None
Optional extension to replace existing one.
debug : str, bool or None
Optional string for debug files in wihch the string is added as postfix.
If True, 'debug' is added.
Returns
-------
filename : str
The standard file name of the requested file type.
"""
if file_type_to_name is None:
file_type_to_name = default_file_type_to_name;
if ftype is None:
fname = directory;
if ftype in file_type_synonyms.keys():
ftype = file_type_synonyms[ftype];
if ftype == 'expression' or expression is not None:
expression = te.Expression(expression);
fname = expression.string(values=values);
#Note: expressions are used for raw data only atm -> no prefix, debug
prefix = None;
debug = None;
else:
fname = file_type_to_name.get(ftype, None);
e = te.Expression(fname);
if len(e.tags) > 0:
fname = e.string(values=values);
#Note: expressions are used for raw data only atm -> no prefix, debug
prefix = None;
debug = None;
if fname is None:
raise ValueError('Cannot find name for type %r!' % ftype);
if prefix and prefix != '':
if isinstance(prefix, list):
prefix = '_'.join(prefix);
fname = prefix + '_' + fname;
if postfix is not None and postfix != '':
if isinstance(postfix, list):
postfix = '_'.join(postfix);
fname = fname.split('.');
fname = '.'.join(fname[:-1]) + '_' + postfix + '.' + fname[-1];
if debug:
if not isinstance(debug, str):
debug = 'debug';
#fname = fname.split('.');
#fname = '.'.join(fname[:-1]) + '_' + debug + '.' + fname[-1];
fname = debug + '_' + fname;
if extension:
fname = fname.split('.');
fname = '.'.join(fname[:-1] + [extension]);
if directory:
fname = io.join(directory, fname);
return fname;
__author__ = 'Christoph Kirst <*****@*****.**>'
__license__ = 'GPLv3 - GNU General Pulic License v3 (see LICENSE)'
__copyright__ = 'Copyright © 2020 by Christoph Kirst'
__webpage__ = 'http://idisco.info'
__download__ = 'http://www.github.com/ChristophKirst/ClearMap2'
import ClearMap.IO.IO as io
###############################################################################
### Files
###############################################################################
base_directory = io.split(io.abspath(__file__))[0]
"""The base directory for test data."""
data_directory = io.join(base_directory, 'Data')
"""The base directory for test data."""
vasculature_directory = io.join(data_directory, 'Vasculature')
"""Directory for vasculature sample data."""
vasculature_raw = io.join(vasculature_directory, 'vasculature_raw.npy')
"""Vasculature sample data."""
vasculature_pre = io.join(vasculature_directory, 'vasculature_pre.npy')
"""Vasculature sample data."""
vasculature_surface_raw = io.join(vasculature_directory,
'vasculature_surface_raw.npy')
"""Vasculature sample data."""
